Aluminum (Al) and manganese (Mn) toxicity are the top two constraints of crop production in acid soil. Crops have evolved common and specific mechanisms to tolerate the two stresses. In the present study, the responses (toxicity and tolerance) of near-isogenic wheat lines (ET8 and ES8) and their parents (Carazinho and Egret) to Al and Mn were compared by determining the physiological parameters and conducting transcriptome profiling of the roots. The results showed the following: (1) Carazinho and ET8 exhibited dual tolerance to Al and Mn compared to Egret and ES8, indicated by higher relative root elongation and SPAD. (2) After entering the roots, Al was mainly distributed in the roots and fixed in the cell wall, while Mn was mainly distributed in the cell sap and then transported to the leaves. Both Al and Mn stresses decreased the contents of Ca, Mg, and Zn; Mn stress also inhibited the accumulation of Fe, while Al showed an opposite effect. (3) A transcriptomic analysis identified 5581 differentially expressed genes (DEGs) under Al stress and 4165 DEGs under Mn stress. Among these, 2774 DEGs were regulated by both Al and Mn stresses, while 2280 and 1957 DEGs were exclusively regulated by Al stress and Mn stress, respectively. GO and KEGG analyses indicated that cell wall metabolism responds exclusively to Al, while nicotianamine synthesis exclusively responds to Mn. Pathways such as signaling, phenylpropanoid metabolism, and metal ion transport showed commonality and specificity to Al and Mn. Transcription factors (TFs), such as MYB, WRKY, and AP2 families, were also regulated by Al and Mn, and a weighted gene co-expression network analysis (WGCNA) identified PODP7, VATB2, and ABCC3 as the hub genes for Al tolerance and NAS for Mn tolerance. The identified genes and pathways can be used as targets for pyramiding genes and breeding multi-tolerant varieties.

This meta-analysis combined the results of 61 independent studies published in 2005–2025 to examine polyamine-mediated responses to aluminum, cadmium, lead, chromium, copper, manganese, and selenium stress in plants. The logarithm ratio of responses (lnRR) under the random-effects model was used to calculate the effect sizes. Polyamine application significantly (p < 0.001) enhanced plant growth, with strong increases in root elongation (lnRR = 0.490, 95% CI: 0.362–0.618), fresh weight (lnRR = 0.413, 95% CI: 0.347–0.480), and dry weight (lnRR = 0.475, 95% CI: 0.409–0.541). Oxidative stress was markedly reduced, as reflected by decreases in reactive oxygen species accumulation (lnRR = −0.585, 95% CI −0.682 to −0.487, p < 0.001), hydrogen peroxide content (lnRR = 0.005, 95% CI −0.244 to 0.254, p = 0.968), and lipid peroxidation (lnRR = −0.487, 95% CI −0.578 to −0.397, p < 0.001). The antioxidant defenses were strengthened, and the levels of superoxide dismutase (lnRR = 0.468, p < 0.001) and catalase activity (lnRR = 0.373, p < 0.001) increased significantly. Metal accumulation was consistently reduced in polyamine-treated plants (lnRR = −0.392, 95% CI −0.460 to −0.324, p < 0.001). Supplementary genetic-level data indicated that metal stress triggers polyamines to regulate metal transporters, polyamine biosynthesis genes, antioxidant-related genes, and hormone-signaling pathways. Collectively, these data points make polyamines a key controller of plant metal stress tolerance and offer a quantitative and mechanistic system to apply them to metal-impacted agroecosystems.

Aluminum (Al) and manganese (Mn) toxicity are the top two constraints to crop production in acid soil. Crops have evolved common and specific mechanisms to tolerate the two stresses. In the present study, the responses (toxicity and tolerance) of wheat near-isogenic lines (ET8 and ES8) and their parents (Carazinho and Egret) to Al and Mn were compared by determining physiolog-ical parameters and transcriptome profiling of roots. The results showed that: (1) Carazinho and ET8 exhibited dual tolerance to Al and Mn as compared with Egret and ES8, indicated by higher relative root elongation and SPAD; (2) After entering into roots, Al was mainly distributed in the root and fixed in the cell wall, while Mn was mainly distributed in the cell sap and then trans-ported to leaves. Both Al and Mn stresses decreased the contents of Ca, Mg, and Zn; Mn stress al-so inhibited the accumulation of Fe, while Al showed an opposite effect; (3) Transcriptomic analy-sis identified 5581 differentially expressed genes (DEGs) under Al stress and 4165 DEGs under Mn stress. Among these, 2774 DEGs were regulated by both Al and Mn stresses, while 2280 and 1957 DEGs were exclusively regulated by Al and Mn stress, respectively. GO and KEGG analyses indi-cated that cell wall metabolism responds exclusively to Al, while nicotianamine synthesis exclu-sively responds to Mn. Pathways such as signaling, phenylpropanoid metabolism, and metal ion transport showed commonality and specificity to Al and Mn. TFs, such as MYB, WRKY, and AP2 families, were also regulated by Al and Mn, and WGCNA identified PODP7, VATB2, and ABCC3 as the hub genes for Al tolerance and NAS for Mn tolerance. The identified genes and pathways can be used as targets for pyramiding genes and breeding multi-tolerant varieties.

Soil acidity is a major constraint in many agricultural regions, where increased aluminum (Al³⁺) solubility at low pH severely affects plant health by inhibiting root elongation, disrupting nutrient uptake, and inducing oxidative stress. Recent studies have highlighted melatonin, a widely occurring indoleamine with strong antioxidant and stress-modulating properties, which alleviates Al-induced damage in crops. This review synthesizes current physiological, biochemical, and agronomic evidence demonstrating that exogenous melatonin enhances plant tolerance to aluminum toxicity. Across multiple model and crop species, melatonin application has been shown to improve root elongation by 20–45%, reduce lipid peroxidation by 30–60%, and enhance key antioxidant enzymes such as SOD, POD, and CAT by 25–70% under Al stress. Case studies in soybean, wheat, maize, and rice further indicate that melatonin protects root meristems from oxidative damage, stabilizes photosynthetic machinery, and improves nutrient acquisition. In acidic soils (pH 4.5), melatonin-treated soybean exhibited 28% greater biomass and 15–22% higher N and P uptake, while wheat plants demonstrated 10–18% higher grain filling under field-simulated Al stress. Emerging long-term studies show that melatonin also benefits soil health. Multi season experiments reveal that melatonin enhances root exudates that support beneficial rhizosphere microbes, increases soil enzymatic activities (urease, phosphatase) by 20–35%, and lowers exchangeable Al by 12–18%. These improvements contribute to cumulative yield gains of 10–18% over successive cropping cycles. Additionally, genetic approaches aimed at increasing endogenous melatonin levels in plants have demonstrated 12–30% yield improvement in acid soil conditions. This review highlights the need for multi-year, multi-location studies to further clarify how melatonin can support sustainable agricultural practices, enhance soil fertility, and mitigate aluminum toxicity in acid-affected regions.